Re: AMBER: Bad atom symbol, K+ and IB in vacuum

From: David A. Case <>
Date: Wed, 31 Mar 2004 10:38:47 -0800

On Tue, Mar 30, 2004, Skauge Tormod wrote:
> I'm trying to run a simulation of a RNA in vacuum. As recommended in the
> amber DNA tutorial, I want to include a larger and softer counterion
> than Na+ and have tried K+ and IB. Running sander for the heating
> process (to 300K) fails with the comment "bad atom symbol: I" or "bad
> atom symbol: K".

> The "testrun" file:
> test to see if IB and K+ works
> &cntrl
> IMIN=0, NTX=1, IREST=0, NSNB=99999,
> TIMLIM=300, IG=71277, IBELLY=0,
> IGB=1, NTB=0, GBPARM=2, GBSA=0,

You say that you want to run RNA in vacuum (which I don't think is _really_
recommended in the DNA tutorial or anywhere else), yet you set igb=1, which
requests a generalized Born simulation. GB simulations are not set up to use
counterions, as counterions are treated as a part of the solvent, not part of
the solute.

You could set igb=0 to indeed get a vacuum simulation, but I cannot in good
conscience actually recommend this. Either using an explicit water or a
generalized Born model should be much better.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Wed Mar 31 2004 - 19:53:00 PST
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